HEADER CHAPERONE 08-JUN-17 5XR9 TITLE CRYSTAL STRUCTURE OF HUMAN HSP90 WITH FS6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAT SHOCK PROTEIN HSP 90-ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 9-236; COMPND 5 SYNONYM: HEAT SHOCK 86 KDA,HSP86,LIPOPOLYSACCHARIDE-ASSOCIATED COMPND 6 PROTEIN 2,LPS-ASSOCIATED PROTEIN 2,RENAL CARCINOMA ANTIGEN NY-REN-38; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HSP90AA1, HSP90A, HSPC1, HSPCA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEAT SHOCK PROTEIN HSP 90, INHIBITOR, COMPLEX, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR J.LI,F.SHI,B.XIONG,J.H.HE REVDAT 2 27-MAR-24 5XR9 1 REMARK REVDAT 1 20-JUN-18 5XR9 0 JRNL AUTH J.LI,F.SHI,B.XIONG,J.H.HE JRNL TITL CRYSTAL STRUCTURE OF HUMAN HSP90 WITH FS6 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.2_432 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 47132 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1952 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.6209 - 3.2329 0.99 4765 203 0.1811 0.1929 REMARK 3 2 3.2329 - 2.5664 1.00 4655 198 0.1956 0.2012 REMARK 3 3 2.5664 - 2.2420 1.00 4603 199 0.1913 0.2079 REMARK 3 4 2.2420 - 2.0371 1.00 4591 194 0.1770 0.1702 REMARK 3 5 2.0371 - 1.8911 0.99 4554 198 0.1742 0.1850 REMARK 3 6 1.8911 - 1.7796 0.99 4477 203 0.1745 0.2079 REMARK 3 7 1.7796 - 1.6905 0.98 4470 191 0.1739 0.1938 REMARK 3 8 1.6905 - 1.6169 0.97 4449 186 0.1753 0.1894 REMARK 3 9 1.6169 - 1.5546 0.96 4350 191 0.1830 0.2028 REMARK 3 10 1.5546 - 1.5010 0.94 4266 189 0.1999 0.2277 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 39.61 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.27670 REMARK 3 B22 (A**2) : -0.15680 REMARK 3 B33 (A**2) : -1.11990 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1689 REMARK 3 ANGLE : 1.057 2279 REMARK 3 CHIRALITY : 0.075 258 REMARK 3 PLANARITY : 0.006 289 REMARK 3 DIHEDRAL : 15.133 629 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -0.4661 -30.7054 -20.5189 REMARK 3 T TENSOR REMARK 3 T11: 0.0933 T22: 0.0787 REMARK 3 T33: 0.0953 T12: -0.0066 REMARK 3 T13: -0.0014 T23: 0.0173 REMARK 3 L TENSOR REMARK 3 L11: 1.1205 L22: 0.7335 REMARK 3 L33: 0.9942 L12: -0.2911 REMARK 3 L13: -0.0556 L23: -0.1002 REMARK 3 S TENSOR REMARK 3 S11: -0.0124 S12: -0.0236 S13: 0.0269 REMARK 3 S21: -0.0038 S22: 0.0043 S23: -0.0241 REMARK 3 S31: -0.0319 S32: -0.0139 S33: 0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5XR9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1300004018. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48036 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.501 REMARK 200 RESOLUTION RANGE LOW (A) : 33.612 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-25%(W/V) PEG 2000 MONOMETHYL ETHER, REMARK 280 200MM MAGNESIUM CHLORIDE, 100MM SODIUM CACODYLATE, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 33.61250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.26200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.01250 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.61250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.26200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.01250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.61250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.26200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.01250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.61250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.26200 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.01250 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASP A 9 REMARK 465 GLN A 10 REMARK 465 PRO A 11 REMARK 465 MET A 12 REMARK 465 GLU A 13 REMARK 465 GLU A 14 REMARK 465 GLU A 15 REMARK 465 GLU A 16 REMARK 465 GLU A 225 REMARK 465 ARG A 226 REMARK 465 ASP A 227 REMARK 465 LYS A 228 REMARK 465 GLU A 229 REMARK 465 VAL A 230 REMARK 465 SER A 231 REMARK 465 ASP A 232 REMARK 465 ASP A 233 REMARK 465 GLU A 234 REMARK 465 ALA A 235 REMARK 465 GLU A 236 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR A 38 109.15 -161.43 REMARK 500 THR A 94 40.23 -108.10 REMARK 500 ASN A 105 -44.75 -131.12 REMARK 500 ALA A 166 -145.93 66.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8CU A 301 DBREF 5XR9 A 9 236 UNP P07900 HS90A_HUMAN 9 236 SEQRES 1 A 228 ASP GLN PRO MET GLU GLU GLU GLU VAL GLU THR PHE ALA SEQRES 2 A 228 PHE GLN ALA GLU ILE ALA GLN LEU MET SER LEU ILE ILE SEQRES 3 A 228 ASN THR PHE TYR SER ASN LYS GLU ILE PHE LEU ARG GLU SEQRES 4 A 228 LEU ILE SER ASN SER SER ASP ALA LEU ASP LYS ILE ARG SEQRES 5 A 228 TYR GLU SER LEU THR ASP PRO SER LYS LEU ASP SER GLY SEQRES 6 A 228 LYS GLU LEU HIS ILE ASN LEU ILE PRO ASN LYS GLN ASP SEQRES 7 A 228 ARG THR LEU THR ILE VAL ASP THR GLY ILE GLY MET THR SEQRES 8 A 228 LYS ALA ASP LEU ILE ASN ASN LEU GLY THR ILE ALA LYS SEQRES 9 A 228 SER GLY THR LYS ALA PHE MET GLU ALA LEU GLN ALA GLY SEQRES 10 A 228 ALA ASP ILE SER MET ILE GLY GLN PHE GLY VAL GLY PHE SEQRES 11 A 228 TYR SER ALA TYR LEU VAL ALA GLU LYS VAL THR VAL ILE SEQRES 12 A 228 THR LYS HIS ASN ASP ASP GLU GLN TYR ALA TRP GLU SER SEQRES 13 A 228 SER ALA GLY GLY SER PHE THR VAL ARG THR ASP THR GLY SEQRES 14 A 228 GLU PRO MET GLY ARG GLY THR LYS VAL ILE LEU HIS LEU SEQRES 15 A 228 LYS GLU ASP GLN THR GLU TYR LEU GLU GLU ARG ARG ILE SEQRES 16 A 228 LYS GLU ILE VAL LYS LYS HIS SER GLN PHE ILE GLY TYR SEQRES 17 A 228 PRO ILE THR LEU PHE VAL GLU LYS GLU ARG ASP LYS GLU SEQRES 18 A 228 VAL SER ASP ASP GLU ALA GLU HET 8CU A 301 26 HETNAM 8CU N-[3-[5-BROMANYL-2,4-BIS(OXIDANYL)PHENYL]-4-(4- HETNAM 2 8CU METHOXYPHENYL)-1,2-OXAZOL-5-YL]ETHANAMIDE FORMUL 2 8CU C18 H15 BR N2 O5 FORMUL 3 HOH *175(H2 O) HELIX 1 AA1 GLN A 23 THR A 36 1 14 HELIX 2 AA2 GLU A 42 LEU A 64 1 23 HELIX 3 AA3 THR A 65 ASP A 71 5 7 HELIX 4 AA4 THR A 99 ASN A 105 1 7 HELIX 5 AA5 ASN A 105 ALA A 124 1 20 HELIX 6 AA6 ASP A 127 GLY A 135 5 9 HELIX 7 AA7 VAL A 136 LEU A 143 5 8 HELIX 8 AA8 GLN A 194 LEU A 198 5 5 HELIX 9 AA9 GLU A 199 SER A 211 1 13 SHEET 1 AA1 8 GLU A 18 ALA A 21 0 SHEET 2 AA1 8 SER A 169 THR A 174 -1 O PHE A 170 N PHE A 20 SHEET 3 AA1 8 GLN A 159 SER A 164 -1 N ALA A 161 O ARG A 173 SHEET 4 AA1 8 ALA A 145 LYS A 153 -1 N VAL A 150 O TRP A 162 SHEET 5 AA1 8 GLY A 183 LEU A 190 -1 O ILE A 187 N THR A 149 SHEET 6 AA1 8 THR A 88 ASP A 93 -1 N LEU A 89 O LEU A 188 SHEET 7 AA1 8 ILE A 78 ASN A 83 -1 N ILE A 81 O THR A 90 SHEET 8 AA1 8 ILE A 218 LEU A 220 1 O THR A 219 N LEU A 80 SITE 1 AC1 15 ASN A 51 SER A 52 ALA A 55 LYS A 58 SITE 2 AC1 15 ASP A 93 ILE A 96 GLY A 97 MET A 98 SITE 3 AC1 15 PHE A 138 THR A 184 VAL A 186 HOH A 403 SITE 4 AC1 15 HOH A 421 HOH A 457 HOH A 484 CRYST1 67.225 90.524 98.025 90.00 90.00 90.00 I 2 2 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014875 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011047 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010201 0.00000